public void TestShiftReactionVerticalTwohorizontalmolecules()
{
var atom1 = builder.NewAtom("C");
atom1.Point2D = Vector2.Zero;
var atom2 = builder.NewAtom("C");
atom2.Point2D = new Vector2(1, 0);
var react1 = builder.NewAtomContainer();
var reaction = builder.NewReaction();
reaction.Reactants.Add(react1);
react1.Atoms.Add(atom1);
react1.Atoms.Add(atom2);
react1.AddBond(react1.Atoms[0], react1.Atoms[1], BondOrder.Single);
var reaction2 = (IReaction)reaction.Clone();
var react2 = reaction2.Reactants[0];
// shift the second reaction up
GeometryUtil.ShiftReactionVertical(reaction2, GeometryUtil.GetMinMax(react2), GeometryUtil.GetMinMax(react1),
1.0);
// assert all coordinates of the second reaction moved up
AtomContainerDiff.Diff(react1, react2);
for (int i = 0; i < 2; i++)
{
atom1 = react1.Atoms[0];
atom2 = react2.Atoms[0];
// so, x coordinates should be the same
Assert.AreEqual(atom1.Point2D.Value.X, atom2.Point2D.Value.X, 0.0);
// but, y coordinates should not
Assert.IsTrue(atom1.Point2D.Value.Y < atom2.Point2D.Value.Y);
}
}
public void TestShiftContainerHorizontalTwoverticalmolecules()
{
var atom1 = builder.NewAtom("C");
atom1.Point2D = Vector2.Zero;
var atom2 = builder.NewAtom("C");
atom2.Point2D = new Vector2(0, 1);
var react1 = builder.NewAtomContainer();
react1.Atoms.Add(atom1);
react1.Atoms.Add(atom2);
var react2 = (IAtomContainer)react1.Clone();
// shift the second molecule right
GeometryUtil.ShiftContainer(react2, GeometryUtil.GetMinMax(react2), GeometryUtil.GetMinMax(react1), 1.0);
// assert all coordinates of the second molecule moved right
AtomContainerDiff.Diff(react1, react2);
for (int i = 0; i < 2; i++)
{
atom1 = react1.Atoms[0];
atom2 = react2.Atoms[0];
// so, y coordinates should be the same
Assert.AreEqual(atom1.Point2D.Value.Y, atom2.Point2D.Value.Y, 0.0);
// but, x coordinates should not
Assert.IsTrue(atom1.Point2D.Value.X < atom2.Point2D.Value.X);
}
}
public void EnsureConsistentRepresentation()
{
IAtomContainer a = CreateFromSmiles("C1=CC2=CC3=CC4=C(C=CC=C4)C=C3C=C2C=C1");
IAtomContainer b = CreateFromSmiles("c1cc2cc3cc4c(cccc4)cc3cc2cc1");
Aromaticity arom = new Aromaticity(ElectronDonation.DaylightModel, Cycles.AllSimpleFinder);
arom.Apply(a);
arom.Apply(b);
Assert.IsTrue(AtomContainerDiff.Diff(a, b).Count() == 0);
}
public void TestCalculate_NoModifications()
{
var mol = SomeoneBringMeSomeWater();
var clone = (IAtomContainer)mol.Clone();
CreateDescriptor().Calculate(mol);
var diff = AtomContainerDiff.Diff(clone, mol);
Assert.AreEqual(0, diff.Length, $"The descriptor must not change the passed molecule in any respect, but found this diff: {diff}");
}
public void TestMoleculeInvariance()
{
var mol = TestMoleculeFactory.MakePyrrole();
var clone = (IAtomContainer)mol.Clone();
// should pass since we have not explicitly detected aromaticity
foreach (var atom in mol.Atoms)
{
Assert.IsFalse(atom.IsAromatic);
}
var diff1 = AtomContainerDiff.Diff(mol, clone);
Assert.AreEqual("", diff1);
var fprinter = new ExtendedFingerprinter();
var fp = fprinter.GetBitFingerprint(mol).AsBitSet();
Assert.IsNotNull(fp);
var diff2 = AtomContainerDiff.Diff(mol, clone);
Assert.IsTrue(diff2.Length == 0, "There was a difference\n" + diff2);
}